Available tools and plugins:

We are (slowly) transitioning our tools and plugins to the lab Github.
Please follow the links below for most up to date versions of each of the tools.

Where relevant please cite originating papers
For bugs/issues and queries please contact the lab here

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HIT-MAP
Automated annotation and visualisation of high-resolution
spatial proteomic mass spectrometry imaging data

Platform: R (Windows, MacOS and Linux)
Now available on Github

Also available as a Docker Image here

Citation:
Guo G*, Papanicolaou M* et al. Nature Communications (2021)

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Platform: Standalone Windows and MacOS application
http://galene.flimfit.org/

Citation:
Warren SC et al. eLife (2018) PubMed

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Automated ECM fibre orientation and alignment script

Platform: FIJI / ImageJ
Now available on Github

Citation:
Mayorca-Guiliani AE*, Madsen CD*, Cox TR* et al. Nature Medicine (2017) PubMed

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Automated Picrosirius Red (PR) analysis of collagen I using transmitted light

Platform: FIJI / ImageJ
Download v1.11

Citation:
Vennin C et al. Nature Communications (2019) PubMed

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Automated Picrosirius Red (PR) birefringence (BRF) analysis of collagen I using polarised light

Platform: FIJI / ImageJ
Now available on Github

Citation:
Vennin C et al. Nature Communications (2019) PubMed

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Automated Masson’s Trichrome Analysis of collagen I/bone (blue)

Platform: FIJI / ImageJ
Download v1.03

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